Baptista, Inês S. C.Kandavalli, VinodhChauhan, VatsalaBahrudeen, Mohamed N. M.Almeida, Bilena L. B.Palma, Cristina S. D.Dash, SuchintakRibeiro, André S.2022-09-052022-09-052022-041874-9399PURE: 46295225PURE UUID: fab6387b-972f-44ec-8f65-38e0b765c86eScopus: 85127225517PubMed: 35338024WOS: 000791277200001http://hdl.handle.net/10362/143501Funding Information: This work was supported by the Jane and Aatos Erkko Foundation [ 10-10524-38 to A.S.R]; Finnish Cultural Foundation [ 00200193 and 00212591 to I.S.C.B., and 50201300 to S.D.]; Pirkanmaa Regional Fund of the Finnish Cultural Foundation to V.K.; Suomalainen Tiedeakatemia to C.S.D.P.; Tampere University Graduate Program to V.C., M.N.M.B., and B.L.B.A.; EDUFI Fellowship [TM-19-11105 to S.D]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: © 2022 The AuthorsEscherichia coli uses σ factors to quickly control large gene cohorts during stress conditions. While most of its genes respond to a single σ factor, approximately 5% of them have dual σ factor preference. The most common are those responsive to both σ70, which controls housekeeping genes, and σ38, which activates genes during stationary growth and stresses. Using RNA-seq and flow-cytometry measurements, we show that ‘σ70+38 genes’ are nearly as upregulated in stationary growth as ‘σ38 genes’. Moreover, we find a clear quantitative relationship between their promoter sequence and their response strength to changes in σ38 levels. We then propose and validate a sequence dependent model of σ70+38 genes, with dual sensitivity to σ38 and σ70, that is applicable in the exponential and stationary growth phases, as well in the transient period in between. We further propose a general model, applicable to other stresses and σ factor combinations. Given this, promoters controlling σ70+38 genes (and variants) could become important building blocks of synthetic circuits with predictable, sequence-dependent sensitivity to transitions between the exponential and stationary growth phases.93433144engDual σ factor preferenceE. coliFlow cytometryRNA-seqSequence-dependent gene expression modelBiophysicsStructural BiologyBiochemistryMolecular BiologyGeneticsjournal article10.1016/j.bbagrm.2022.194812https://www.scopus.com/pages/publications/85127225517